I don't think it's that difficult to do something like what is mentioned in the original article. Everyone needs to understand that the "chips" we see on circuit boards aren't the real chip. The actual die inside the package is much smaller than what we see on a board. The die can be as small as .1mm square. The dies are placed into much larger packages so that they can be soldered to a circuit board.
If properly done, a die could be placed between layers like an embedded via. It would take a great deal of knowledge and skill to do it, but it could be done. With some of the innovative assembly techniques being developed by companies like Apple (as much as I dislike Apple), the Chinese contract manufacturers have been taught how to do some crazy things.
Tapping something like an SPI bus isn't that hard. It's only 4 signals. One could create a chip that would normally be a pass-through, but would change commands when it needed to. I have done quite a bit of SPI software and hardware, and I can see how this could be done. It would be rally hard, but when state sponsored, it's possible.
Our government would not even blink at spending $100 million on something like this. With that kind of money, it would be easy to find a few very talented engineers that could pull this off.
I remember back in the 90's people were opening up ICs and probing them under a microscope in live running circuits to break the encryption on satellite TV receivers. If people will do this to get free TV channels, what do you think a government with nearly unlimited funds can do?